draw.oncoprint: Draw Oncoprint Plot to display the mutation information

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Draw Oncoprint Plot to display the mutation information

Description

draw.oncoprint plots the heatmap to display the mutation information for samples.

Usage

draw.oncoprint(
  phenotype_info = NULL,
  Missense_column = NULL,
  Missense_label = NULL,
  Amplification_column = NULL,
  Amplification_label = NULL,
  Deletion_column = NULL,
  Deletion_label = NULL,
  Sample_column = NULL,
  main = "",
  pdf_file = NULL,
  ...
)

Arguments

phenotype_info	data.frame, phenotype of samples. Users can call Biobase::pData(eset) to create.
Missense_column	character, column names from phenotype_info.
Missense_label	character, gene label for the Missense_column.
Amplification_column	character, column names from phenotype_info.
Amplification_label	character, gene label for the Amplification_column.
Deletion_column	character, column names from phenotype_info.
Deletion_label	character, gene label for the mDeletion_column.
Sample_column	character, column names from phenotype_info. If not NULL, will show sample names in the figure.
main	character, an overall title for the plot. Default is "".
pdf_file	character, the file path to save plot as PDF file. If NULL, no PDF file will be saved. Default is NULL.
...	for more options, please check ?oncoPrint for more details.

Value

Return a logical value. If TRUE, the plot has been created successfully.

Examples

all_sample <- sprintf('Sample%s',1:30)
group1_sample <- sample(all_sample,18) ## demo sample for KRAS missense mutation
group2_sample <- sample(all_sample,12) ## demo sample for MYC amplification
group3_sample <- sample(all_sample,10) ## demo sample for MYC missense mutation
group4_sample <- sample(all_sample,1) ## demo sample for MYC deletion
phenotype_info_demo <-
  data.frame(sample =sprintf('Sample%s',1:30),
             KRAS_MIS=ifelse(all_sample %in% group1_sample,1,0),
             MYC_AMP=ifelse(all_sample %in% group2_sample,1,0),
             MYC_MIS=ifelse(all_sample %in% group3_sample,1,0),
             MYC_DEL=ifelse(all_sample %in% group4_sample,1,0))
draw.oncoprint(phenotype_info=phenotype_info_demo,
               Missense_column=c('KRAS_MIS','MYC_MIS'),Missense_label=c('KRAS','MYC'),
               Amplification_column=c('MYC_AMP'),Amplification_label=c('MYC'),
               Deletion_column=c('MYC_DEL'),Deletion_label=c('MYC'),
               Sample_column='sample',
               main="OncoPrint for the demo dataset")
## Not run: 

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.